DOE OSTI · 3739764
The need for standardization and improved open (meta)data practices in metaproteomics
Abstract
Metaproteomics enables functional insight into microbial communities by identifying and quantifying proteins in complex samples. Yet, heterogeneous analytical workflows and the lack of standardization across experimental and bioinformatics stages hinder reproducibility and comparability, limiting integration with other omics data. We here present a community-developed reporting checklist tailored to the specific needs of metaproteomics. We also outline current efforts to enable structured and interoperable metadata capture, drawing on standards from proteomics and microbiome research wherever possible. By promoting transparent reporting and advancing metadata practices, our recommendations aim to align metaproteomics more closely with FAIR principles and support reproducible and interoperable research practices.
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Armengaud, Jean [Universite Paris-Saclay, France], Perez riverol, Yasset [European Molecular Biology Laboratory, European Bioinformatics], Seifert, Jana [University of Hohenheim, Germany], Grenga, Lucia [Atomic Energy and Alternate Energies Commison], Jehmlich, Nico [Helmholtz Centre for Environmental Research - UFZ, Germany], Arntzen, Magnus [Norwegian University of Life Sciences, Norway], Benndorf, Dirk [University of Magdeburg, Germany], John, Nithu [European Molecular Biology Laboratory, European Bioinformatics Institute], Hettich, Robert {Bob} [ORNL] (ORCID:000000017708786X), Jagtap, Pratik [University of Minnesota, Saint Paul], Heyer, Robert [University of Magdeburg, Germany], Li, Leyuan [Beijing Institute of Lifeomics], Mesuere, Bart [VIB - UGent Center for Medical Biotechnology, Gent, Belgium], Verschaffelt, Pieter [VIB - UGent Center for Medical Biotechnology, Gent, Belgium], Kunath, Benoit [University of Luxembourg], Wolf, Maximilian [University of Magdeburg, Germany], Vizcaino, Juan [European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust ], Uzzau, Sergio [University of Sassari, Italy], Ning, Zhibin [University of Ottawa, Canada], Neely, Benjamin [National Institute of Standards and Technology (NIST), Gaithersburg, MD], Pedersen, Ane [Nestlé Institute of Food Safety & Analytical Sciences, Nestlé Research, Lausanne, Switzerland], Rajan, Jeena [European Molecular Biology Laboratory, European Bioinformatics Institute], Kleiner, Manuel [North Carolina State University]. 2026-07-01. The need for standardization and improved open (meta)data practices in metaproteomics. https://doi.org/10.1186/s40168-026-02455-0
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